On 02/12/2013 10:18 AM, Keith Robison wrote: > How does Ray deal with the mixture of correct (<-- -->, large span) and noise > (--> <--, short span) reads found in a typical mate pair library? Is it
Usually, Ray sees 2 peaks: the noise (---> <---) which contains some useful data, and the large (<--- --->). During the extension of seeds, both peaks are tested and the one that matches is selected for each observed pair. During the scaffolding, the largest is selected. Example in LibraryStatistics.txt: LibraryNumber: 0 InputFormat: TwoFiles,Paired DetectionType: Automatic File: eel/1_American_eel_genome_1_American_eel_genome_4_R1.fastq.gz NumberOfSequences: 183634817 File: eel/1_American_eel_genome_1_American_eel_genome_4_R2.fastq.gz NumberOfSequences: 183634817 Distribution: eel-Ray-polytope-1024-k51-min-length-2013-02-11-1/Library0.txt Peak 0 AverageOuterDistance: 281 StandardDeviation: 102 Peak 1 AverageOuterDistance: 4790 StandardDeviation: 132 >explicitly partitioning/classifying the reads into these categories? > > > On Tue, Feb 12, 2013 at 8:54 AM, Sébastien Boisvert > <[email protected] <mailto:[email protected]>> > wrote: > > > > On 02/12/2013 05:15 AM, frederic texier wrote: > > Bonjour de nouveau, > > > > J'ai un problème quand je veux installer avec l'otpion HAVE_LIBZ=y. > > Faut-il un module supplémentaire à installer avant? > > > > Yes, you need zlib headers. > > On Debian or Ubuntu or other Debian-derived distributions: > > sudo apt-get install -y zlib1g-dev > > > On Fedora or CentOS or other similar distribution: > > sudo yum install -y zlib-devel > > > There is also the option HAVE_LIBBZ2=y that provides native support for > fastq.bz2 files. > > > Je vous remercie. > > Cordialement > > Frédéric Texier. > > > > -----Message d'origine----- > > De : Sébastien Boisvert [mailto:[email protected] > <mailto:[email protected]>] > > Envoyé : vendredi 8 février 2013 18:05 > > À : frederic texier > > Cc : [email protected] > <mailto:[email protected]> > > Objet : Re: Ray output > > > > Bonjour Frédéric, > > > > There is a work-in-progress to add this feature [1], although it's not > in > > the current backlog [2]. > > > > Current available courses of action are: > > > > 1. use -amos option to generate a AMOS file with Ray and then parse > this to > > obtain the information you want (used reads, and so on). > > > > 2. Map your reads on contigs (or on scaffolds) with a aligner and then > pipe > > this in a existing tool (I am sure there exists tools for that that > take a > > SAM file as input). > > > > > > Also, if you want to visualize your assemblies to do some quality > controls > > (usually production departments like to do quality controls), you can > use > > Ray Cloud Browser. > > > > > > Demo: http://genome.ulaval.ca/corbeillab/Ray-Cloud-Browser/ > > Source code: https://github.com/sebhtml/Ray-Cloud-Browser > > Deployment instructions: > > > https://raw.github.com/sebhtml/Ray-Cloud-Browser/master/Documentation/Deploy > > ment.txt > > > > > > --- > > [1] https://github.com/sebhtml/ray/issues/65 > > [2] https://github.com/sebhtml/ray/issues?milestone=5&state=open > > > > > > > > > > Sébastien Boisvert > > Community Manager, Ray Genomics Software Suite PhD student, Université > Laval > > > > On 02/08/2013 09:05 AM, frederic texier wrote: > >> Hello, > >> > >> I have used Ray to assemble bacterial genome but I don't know where > find > > the number of reads really used and the numer of reads not used in the > > output. > >> > >> could you help me to find this, please? > >> > >> Thank you. > >> -- > >> > >> Frédéric Texier > >> > >> Téléphone: +33(0)359317403 <tel:%2B33%280%29359317403> > >> E-mail: [email protected] > <mailto:[email protected]> > >> > >> Genoscreen > >> Campus Pasteur - 1 rue du Pr Calmette > >> 59000 Lille > >> Téléphone: +33(0)320877153 <tel:%2B33%280%29320877153> > >> > >> ********************************************************************** > >> ****** Ce message et toutes les pièces jointes sont confidentiels et > >> établis à l'intention exclusive de son ou ses destinataires. Si vous > >> avez reçu ce message par erreur, merci d'en avertir immédiatement > >> l'émetteur et de détruire le message ainsi que les pièces jointes. > >> Toute modification, édition, utilisation ou diffusion non autorisée > >> est interdite. L'émetteur décline toute responsabilité au titre de ce > >> message s'il a été modifié, déformé, falsifié, infecté par un virus ou > >> encore édité ou diffusé sans autorisation. > >> > >> This message and any attachments are confidential and intended for the > >> named > >> addressee(s) only. > >> If you have received this message in error, please notify immediately > >> the sender, then delete the message and the attachments. Any > >> unauthorized modification, edition, use or dissemination is > >> prohibited. 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